There doesn't seem to be a good way to eliminate the same-finger issue with a Dvorak-style layout without sacrificing finger balance and/or finger preference (i.e., index > middle > ring > pinkie).  For instance, both Dvorak and Colemak tend to use one of the pinkies more than one of the ring fingers (ISTR Dvorak even uses one of the pinkies more than one of the middle fingers).  Surprisingly (to me), even unlocking ZXCV,./; didn't seem to make much difference.

I was able to get same-finger to near-Dvorak levels, but the resultant layouts either felt significantly more awkward or overworked one of the pinkies.

I'm still not very fast with the layout, but I haven't found enough problems with it to give up yet.  (Not just because it's mine, either; I've given up on two of my former layouts already.)  Honestly, I hardly notice the same finger (except with "QUE", which is regrettable).  The heavy index finger use isn't noticeable, either.

I really wish I could have captured into some heuristic what about this layout feels good to me, so I could maybe have made one with more pleasing stats, but I wasn't able to.  :/

EDIT: I wonder how much it has to do with distance.  How do you calculate distance?  Maybe I'll add that to my algorithm and see what it comes up with.  Have you tried optimizing only for distance?  I'm curious what the lower bound is for your corpus.

I can only approximate it by rotating the bottom row, putting "Z" where "B" was, instead of on VK_102.  For Qwerty, it helps a little bit, mostly by helping to balance the load on the left ring and middle fingers with the right ones.  (It also improves "key preference", which is my subjective parameter based on how much I like using each key.)  Colemak is slightly worsened by it, further unbalancing the middle fingers (the right middle finger ends up doing about 16% of all typing, the left, 9%).  (Key preference is improved, though.)  In neither case is same-finger or two-row jumping significantly affected.

So, my algorithm would (kinda-sorta, due to the approximation) say that it's worth it for Qwerty, but not for Colemak.

For poops and giggles, the best single swap on Colemak in my algorithm's opinion is "O" and "S".  This reduces the load on the over-used right pinkie from ~8.5% to ~6.7% (left pinkie does ~7.4%) and increases the load on the under-used left middle finger from ~10.5% to ~12.3% (the right middle finger does ~16%).  Same-hand same-finger is increased, but "persistent same-finger" (like WORD on Colemak) is decreased.  (Personally, I think "WORD" is more awkward after the swap, but whatever).

A comment about awkwardness--I've noticed that row changes involving the middle and ring fingers tend to feel particularly awkward to me.  This is true even of sequences like "WAS" and "FAR" on Colemak.  I think the middle and ring fingers must be bound by the same tendon or ligament, making independent movement of those fingers difficult.  Two-row jumps involving those two fingers are particularly heinous.  Maybe I should plug that into my algorithm and see what happens.

No, I don't understand.  Anyway, there's no parameter for this in my program; I didn't want to get too far away from standard keyboard usage.

Well, I added a parameter for minimizing "bad finger sequences," like QS, SE, WD, and DR on Qwerty.  It has helped quite a bit.

I've also added a couple of Dvorak-inspired parameters that have helped a lot:  one maximizes hand alternation and the other maximizes inward typing.  Both of these things work to minimize "reversals."

Formerly, I was getting better-feeling layouts by locking the "Qwerty keys" (ZXCV and punctuation) prior to optimization.  Now, the opposite is true.  Also, now layouts with the best overall score really are better overall!  So, my parameter set seems to have vastly improved in quality of late.  :)

Currently, my program thinks the best single swap for Colemak is the rather unexpected A/O swap.  This really improves inward flow, but it also eliminates some "bad finger sequences" and balances the load between the pinkies a little better.  Common words like WAS and YOU become a lot easier to type.  (Another interesting example is ORANGE.)  'Course, you lose the left hand Ctrl+A.

Nah, that's just the one swap that results in the greatest improvement (according to my program).  There's a lot more it could do.